Fig. 2
From: T3E: a tool for characterising the epigenetic profile of transposable elements using ChIP-seq data
Uniform background distribution creates artifact enrichments for TEs. A Each dot represents a TE family/subfamily; TEs with unknown classification are reported as “Unknown”. Fold-Changes (FC) were calculated as the ratio between the average number of read mappings to a TE family/subfamily across 100 simulations that assume a uniform distribution of the mappings in the genome and the number of read mappings for the input control library. Dashed lines show a log2 FC = 0. Seven ChIP-seq input control experiments (Dataset 1) are presented. Outliers in four of seven input controls are highlighted. Several TE families/subfamilies presented deviations in the expected number of read mappings from the input control library using uniform background distribution approach. B Numbers of individual copies and their average lengths for distinct TE families/subfamilies in the human genome. Four underestimated and four overestimated TE families/subfamilies are highlighted with the colours of their classification in the boxplot